In high school we studied the inheritance of eye color, as it was explained to us in the most simple way: blue eye color is a recessive, monogenic, autosomal trait. Now I know that it is a bit more complicated than that; there are several genes which determine the inheritance of eye color. That's as far as I my knowledge goes.

Which are these genes and what do they encode for? How is the eye color trait inherited? Provided that a man with blue eyes and a woman with brown eyes have a child, can the probability of their child to have blue eyes be calculated?

2 Answers
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It is mainly determined by the OCA2 gene, but it also likely involves several other genes, including TYR, TYRP1, HERC2, and several others. To complicate things further, it is not a "mutant/wild type" trait, but multiple normal alleles can be found in the population, and it is believed that the sum of these single nucleotide polymorphisms (SNPs) determine the final phenotype.

This answer is so close to be good... why don't you expand a little on what those genes do and how they influence color? I know you linked the papers but it would be much nicer if the answer were self-sufficient. For instance you could say that OCA2 encodes for the P protein, a (supposed) Tyr transporter that allows Tyr, a precursor of the brown pigment melanin, to get into the cells.
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nicoJan 21 '12 at 8:55

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@aleadam Thanks for your answer, it really looks promising, but I was about to ask you the same thing as nico did: can you please expand it and make it more clear and easy to read and understand?
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Gergana VandovaJan 21 '12 at 20:41

The known Human Eye color genes are: EYCL1 (also called gey), the Green/blue eye color gene,
located on chromosome 19 (though there is
also evidence that another gene with similar activity exists but is
not on chromosome 19). EYCL2 (also called bey1), the central brown eye
color gene, possibly located on chromosome 15. EYCL3 (also called
bey2), the Brown/blue eye color gene located on chromosome 15. EYCL3
probably involves mutations in the regulatory region just before the
OCA2 gene (which produces a protein that is expressed in melanocytes).
A second gene for green has also been postulated. Other eye colors
including grey and hazel are not yet explained. We do not yet know
what these genes make, or how they produce eye colors. The two gene
model (EYCL1 and EYCL3) used above explains only a portion of human
eye color inheritance. Both additional eye color genes and modifier
genes are almost certainly involved.